chr2-88126306-C-A

Variant names:

• chr2-88126306-C-A
• NM_001443.3:c.110G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001443.3(FABP1):​c.110G>T​(p.Gly37Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G37E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FABP1 NM_001443.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

Genes affected

FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1415368).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP1	NM_001443.3	c.110G>T	p.Gly37Val	missense_variant	Exon 2 of 4	ENST00000295834.8	NP_001434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP1	ENST00000295834.8	c.110G>T	p.Gly37Val	missense_variant	Exon 2 of 4	1	NM_001443.3	ENSP00000295834.3
FABP1	ENST00000393750.3	c.110G>T	p.Gly37Val	missense_variant	Exon 2 of 3	2		ENSP00000377351.3
FABP1	ENST00000472846.1	n.152G>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
FABP1	ENST00000495375.1	n.396G>T		non_coding_transcript_exon_variant	Exon 3 of 4	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	19
DANN	Benign	0.93
DEOGEN2	Benign	0.017	T;.
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.36
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.86	D;D
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	1.4	L;.
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.55	N;N
REVEL	Benign	0.053
Sift	Benign	0.55	T;T
Sift4G	Benign	0.20	T;T
Polyphen		0.84	P;B
Vest4		0.41
MutPred		0.45		Loss of disorder (P = 0.0502);Loss of disorder (P = 0.0502);
MVP		0.27
MPC		0.34
ClinPred		0.46	T
GERP RS		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.44
gMVP		0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-88425825;